[BiO BB] how to calculate the atom distance between antigen and antibody

[Mike Marchywka]

> From: floris at crs4.it
> To: bbb at bioinformatics.org
> Date: Tue, 15 Jul 2008 16:33:26 +0200
> Subject: Re: [BiO BB] how to calculate the atom distance between antigen and antibody
>
> Hi Li,
>
> you can do it with PyMol.


I was going to mention that many viewers may have some functionality but I couldn't check Cn3d or RasMol.
Do you know if PyMol will build under cygwin? Last time I looked it didn't.

I would  also mention that the pdb files are ascii and, if you just want to pick some random atoms,  
you could probably use PERL but you'll probably discover
you want molecule/cavity surfaces, and then you will want realistic potentials, then you will want ab initio etc....

I have a molecule viewer here with some links to other viewers ( no PyMol or "O" but they are options ), 

http://www.spottext.com/marchywka/glutp/docs.html

that has source code including a pdb class ( terribly hacked from early testing but a good starting
point if you want something in c++).  I also have cavity code for hard-sphere surfaces in various states of 
development ( you can see the pictures... ).




>
>
> M.
>
>
> Matteo Floris
>
> CRS4 Bioinformatica
> http://www.bioinformatica.crs4.org
> phone: +39 070 9250 422
> fax: +39 070 92433114
> ________________________________
>
>> hello all,
>>
>> I am new in this.
>>
>> If I have 1JPS.pdb, would someone please tell me how to calculate
>> the atom
>> distance between antigen and antibody?
>>
>> Thank you.
>>
>> Li
>> _______________________________________________
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>> BBB at bioinformatics.org
>> http://www.bioinformatics.org/mailman/listinfo/bbb
>
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